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Guo Y, Cen K, Yang S, Mai Y, Hong K. Development and validation of an inflammatory response-related signature in triple negative breast cancer for predicting prognosis and immunotherapy. Front Oncol 2023; 13:1175000. [PMID: 37397391 PMCID: PMC10311032 DOI: 10.3389/fonc.2023.1175000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 05/30/2023] [Indexed: 07/04/2023] Open
Abstract
Background Inflammation is one of the most important characteristics of tumor tissue. Signatures based on inflammatory response-related genes (IRGs) can predict prognosis and treatment response in a variety of tumors. However, the clear function of IRGs in the triple negative breast cancer (TNBC) still needs to be explored. Methods IRGs clusters were discovered via consensus clustering, and the prognostic differentially expressed genes (DEGs) across clusters were utilized to develop a signature using a least absolute shrinkage and selection operator (LASSO). Verification analyses were conducted to show the robustness of the signature. The expression of risk genes was identified by RT-qPCR. Lastly, we formulated a nomogram to improve the clinical efficacy of our predictive tool. Results The IRGs signature, comprised of four genes, was developed and was shown to be highly correlated with the prognoses of TNBC patients. In contrast with the performance of the other individual predictors, we discovered that the IRGs signature was remarkably superior. Also, the ImmuneScores were elevated in the low-risk group. The immune cell infiltration showed significant difference between the two groups, as did the expression of immune checkpoints. Conclusion The IRGs signature could act as a biomarker and provide a momentous reference for individual therapy of TNBC.
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Affiliation(s)
- Yangyang Guo
- Department of Thyroid and Breast Surgery, Ningbo First Hospital, Ningbo, Zhejiang, China
| | - Kenan Cen
- Department of Geriatrics, The Affiliated Hospital of Medical School of Ningbo University, Ningbo, Zhejiang, China
| | - Shi Yang
- Department of Thyroid and Breast Surgery, Ningbo First Hospital, Ningbo, Zhejiang, China
| | - Yifeng Mai
- Department of Geriatrics, The Affiliated Hospital of Medical School of Ningbo University, Ningbo, Zhejiang, China
| | - Kai Hong
- Department of Thyroid and Breast Surgery, Ningbo First Hospital, Ningbo, Zhejiang, China
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Well-TEMP-seq as a microwell-based strategy for massively parallel profiling of single-cell temporal RNA dynamics. Nat Commun 2023; 14:1272. [PMID: 36882403 PMCID: PMC9992361 DOI: 10.1038/s41467-023-36902-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 02/21/2023] [Indexed: 03/09/2023] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) reveals the transcriptional heterogeneity of cells, but the static snapshots fail to reveal the time-resolved dynamics of transcription. Herein, we develop Well-TEMP-seq, a high-throughput, cost-effective, accurate, and efficient method for massively parallel profiling the temporal dynamics of single-cell gene expression. Well-TEMP-seq combines metabolic RNA labeling with scRNA-seq method Well-paired-seq to distinguish newly transcribed RNAs marked by T-to-C substitutions from pre-existing RNAs in each of thousands of single cells. The Well-paired-seq chip ensures a high single cell/barcoded bead pairing rate (~80%) and the improved alkylation chemistry on beads greatly alleviates chemical conversion-induced cell loss (~67.5% recovery). We further apply Well-TEMP-seq to profile the transcriptional dynamics of colorectal cancer cells exposed to 5-AZA-CdR, a DNA-demethylating drug. Well-TEMP-seq unbiasedly captures the RNA dynamics and outperforms the splicing-based RNA velocity method. We anticipate that Well-TEMP-seq will be broadly applicable to unveil the dynamics of single-cell gene expression in diverse biological processes.
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Partial-Methylated HeyL Promoter Predicts the Severe Illness in Egyptian COVID-19 Patients. DISEASE MARKERS 2022; 2022:6780710. [PMID: 35655915 PMCID: PMC9153385 DOI: 10.1155/2022/6780710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 05/06/2022] [Indexed: 11/18/2022]
Abstract
Background To date (14 January 2022), the incidence and related mortality rate of COVID-19 in America, Europe, and Asia despite administrated of billions doses of many approved vaccines are still higher than in Egypt. Epigenetic alterations mediate the effects of environmental factors on the regulation of genetic material causing many diseases. Objective We aimed to explore the methylation status of HeyL promoter, a downstream transcription factor in Notch signal, an important regulator of cell proliferation and differentiation blood, pulmonary epithelial, and nerves cells. Methods Our objective was achieved by DNA sequencing of the product from methyl-specific PCR of HeyL promoter after bisulfite modification of DNA extracted from the blood samples of 30 COVID-19 patients and 20 control health subjects and studying its association with clinical-pathological biomarkers. Results We found that the HeyL promoter was partial-methylated in Egyptian COVID-19 patients and control healthy subjects compared to full methylated one that was published in GenBank. We identified unmethylated CpG (TG) flanking the response elements within HeyL promoter in Egyptian COVID-19 patients and control healthy subjects vs. methylated CpG (CG) in reference sequence (GenBank). Also, we observed that the frequency of partial-methylated HeyL promoter was higher in COVID-19 patients and associated with aging, fever, severe pneumonia, ageusia/anosmia, and dry cough compared to control healthy subjects. Conclusion We concluded that hypomethylated HeyL promoter in Egyptian population may facilitate the binding of transcription factors to their binding sites, thus enhancing its regulatory action on the blood, pulmonary epithelium, and nerves cells in contrast to full methylated one that was published in GenBank; thus, addition of demethylating agents to the treatment protocol of COVID-19 may improve the clinical outcomes. Administration of therapy must be based on determination of methylation status of HeyL, a novel prognostic marker for severe illness in COVID-19 patients.
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Griffith DOL. Genomic and transcriptomic somatic alterations of hepatocellular carcinoma in non-cirrhotic livers. Cancer Genet 2022; 264-265:90-99. [DOI: 10.1016/j.cancergen.2022.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 03/07/2022] [Accepted: 04/20/2022] [Indexed: 11/26/2022]
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The NOTCH3 Downstream Target HEYL Is Required for Efficient Human Airway Basal Cell Differentiation. Cells 2021; 10:cells10113215. [PMID: 34831437 PMCID: PMC8620267 DOI: 10.3390/cells10113215] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 11/05/2021] [Accepted: 11/05/2021] [Indexed: 12/14/2022] Open
Abstract
Basal cells (BCs) are stem/progenitor cells of the mucociliary airway epithelium, and their differentiation is orchestrated by the NOTCH signaling pathway. NOTCH3 receptor signaling regulates BC to club cell differentiation; however, the downstream responses that regulate this process are unknown. Overexpression of the active NOTCH3 intracellular domain (NICD3) in primary human bronchial epithelial cells (HBECs) on in vitro air–liquid interface culture promoted club cell differentiation. Bulk RNA-seq analysis identified 692 NICD3-responsive genes, including the classical NOTCH target HEYL, which increased in response to NICD3 and positively correlated with SCGB1A1 (club cell marker) expression. siRNA knockdown of HEYL decreased tight junction formation and cell proliferation. Further, HEYL knockdown reduced club, goblet and ciliated cell differentiation. In addition, we observed decreased expression of HEYL in HBECs from donors with chronic obstructive pulmonary disease (COPD) vs. normal donors which correlates with the impaired differentiation capacity of COPD cells. Finally, overexpression of HEYL in COPD HBECs promoted differentiation into club, goblet and ciliated cells, suggesting the impaired capacity of COPD cells to generate a normal airway epithelium is a reversible phenotype that can be regulated by HEYL. Overall, our data identify the NOTCH3 downstream target HEYL as a key regulator of airway epithelial differentiation.
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Exosomal lncRNA SCIRT/miR-665 Transferring Promotes Lung Cancer Cell Metastasis through the Inhibition of HEYL. JOURNAL OF ONCOLOGY 2021; 2021:9813773. [PMID: 34349799 PMCID: PMC8328715 DOI: 10.1155/2021/9813773] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 07/07/2021] [Indexed: 12/09/2022]
Abstract
Lung cancer remains the leading cause of cancer-related death worldwide. Recently, extracellular vesicles such as exosomes have attracted considerable interest both as a source for theranostic biomarkers and an essential participant in lung cancer progression. However, how specific exosomal cargos, such as noncoding RNAs, are selectively packaged into exosomes and promote lung cancer progression remains unclear. In this study, we identified miR-665 as the most elevated exosomal miRNA from both non-small-cell lung cancer (NSCLC) and small-cell lung cancer (SCLC) patients. We further demonstrated that lncRNA SCIRT was also increased in cancer cell exosomes and may facilitate the exosomal loading of miR-665 with the help of hnRNPA1. As a consequence, exosomal miR-665 promoted lung cancer cell invasion and migration by targeting Notch downstream transcription factor HEYL. In addition, we found that miR-665 and SCIRT were significantly upregulated in tumor tissue and plasma of patients with lung cancer, and both of them showed increased expression in metastatic disease samples. Our findings suggest that the exosomal transferring of miR-665 and SCIRT is a functional and mechanism-driven pathway that contributes to cancer progression and, thus, may provide novel diagnostic and therapeutic targets for lung cancer.
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Jiang C, Liu Y, Wen S, Xu C, Gu L. In silico development and clinical validation of novel 8 gene signature based on lipid metabolism related genes in colon adenocarcinoma. Pharmacol Res 2021; 169:105644. [PMID: 33940186 DOI: 10.1016/j.phrs.2021.105644] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 03/24/2021] [Accepted: 04/22/2021] [Indexed: 12/13/2022]
Abstract
BACKGROUND Changes in lipid metabolism pathways play a major role in colon carcinogenesis and development. Hence, we conducted a systematic analysis of lipid metabolism-related genes to explore new markers that predict the prognosis of colon adenocarcinoma (COAD). METHODS The non-negative Matrix Factorization (NMF) algorithm was applied to identify the molecular subtypes based on lipid metabolism-related genes. A weighted correlation network analysis (WCGNA) was used to identify co-expressed genes, and Lasso multivariate Cox analysis was performed to build a risk prognosis model. A timer database was used to analyze the immune infiltration of the gene signature and the GSCALite database was used for genome-wide analysis of the gene signature. RESULTS TCGA-COAD samples were divided into 3 subtypes based on lipid metabolism-related genes. 2739 genes were identified by WGCNA analysis. Finally, an 8-gene signature (RTN2, FYN, HEYL, FAM69A, FBXL5, HMGN2, LGALS4, STOX1) was constructed that demonstrated good robustness in different datasets, as well as an independent risk factor for colon cancer patients' prognosis. In addition, our model's predictive efficacy overall was higher than that of the other published models, and the 8 genes' expression analysis indicated that RTN2, HEYL, and STOX1 were all expressed highly significantly in COAD, while FAM69A, FBXL5, LGALS4, FYN and HMGN2 were expressed significantly poorly in cancer tissues, which was confirmed in immunohistochemistry. The 8 genes were expressed significantly differently in COAD immune subtypes and correlated with clinical variables. Genome-wide analysis revealed that the STOX1 mutation frequency was the highest, and genome methylation influenced HEYL, FAM69A, and STOX1 gene expression significantly; further, the expression of HEYL and FBXL5 was correlated positively with Copy number variation (CNV) and was regulated significantly by CNV in most cancers. FBXL5 was correlated significantly with austocystin d and bafilomycin and played an important role in anti-tumor and immunotherapy. The HEYL, FYN, FAM69A, and RTN2 genes' expression was associated with the EMT pathway's activation, while LGALS4 and STOX1 were associated significantly with the EMT pathway's inhibition. CONCLUSION This study constructed an 8-gene signature as a novel marker to predict colon cancer patients' survival.
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Affiliation(s)
- Chunhui Jiang
- Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, China
| | - Ye Liu
- Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, China
| | - Siyuan Wen
- Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, China
| | - Chunjie Xu
- Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, China
| | - Lei Gu
- Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, China.
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Liu J, Dong C, Jiang G, Lu X, Liu Y, Wu H. Transcription factor expression as a predictor of colon cancer prognosis: a machine learning practice. BMC Med Genomics 2020; 13:135. [PMID: 32957968 PMCID: PMC7504662 DOI: 10.1186/s12920-020-00775-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Colon cancer is one of the leading causes of cancer deaths in the USA and around the world. Molecular level characters, such as gene expression levels and mutations, may provide profound information for precision treatment apart from pathological indicators. Transcription factors function as critical regulators in all aspects of cell life, but transcription factors-based biomarkers for colon cancer prognosis were still rare and necessary. METHODS We implemented an innovative process to select the transcription factors variables and evaluate the prognostic prediction power by combining the Cox PH model with the random forest algorithm. We picked five top-ranked transcription factors and built a prediction model by using Cox PH regression. Using Kaplan-Meier analysis, we validated our predictive model on four independent publicly available datasets (GSE39582, GSE17536, GSE37892, and GSE17537) from the GEO database, consisting of 925 colon cancer patients. RESULTS A five-transcription-factors based predictive model for colon cancer prognosis has been developed by using TCGA colon cancer patient data. Five transcription factors identified for the predictive model is HOXC9, ZNF556, HEYL, HOXC4 and HOXC6. The prediction power of the model is validated with four GEO datasets consisting of 1584 patient samples. Kaplan-Meier curve and log-rank tests were conducted on both training and validation datasets, the difference of overall survival time between predicted low and high-risk groups can be clearly observed. Gene set enrichment analysis was performed to further investigate the difference between low and high-risk groups in the gene pathway level. The biological meaning was interpreted. Overall, our results prove our prediction model has a strong prediction power on colon cancer prognosis. CONCLUSIONS Transcription factors can be used to construct colon cancer prognostic signatures with strong prediction power. The variable selection process used in this study has the potential to be implemented in the prognostic signature discovery of other cancer types. Our five TF-based predictive model would help with understanding the hidden relationship between colon cancer patient survival and transcription factor activities. It will also provide more insights into the precision treatment of colon cancer patients from a genomic information perspective.
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Affiliation(s)
- Jiannan Liu
- Depart of BioHealth Informatics, School of Informatics and Computing, Indiana University-Purdue University Indianapolis, Indianapolis, IN, USA
| | - Chuanpeng Dong
- Depart of BioHealth Informatics, School of Informatics and Computing, Indiana University-Purdue University Indianapolis, Indianapolis, IN, USA
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Guanglong Jiang
- Depart of BioHealth Informatics, School of Informatics and Computing, Indiana University-Purdue University Indianapolis, Indianapolis, IN, USA
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Xiaoyu Lu
- Depart of BioHealth Informatics, School of Informatics and Computing, Indiana University-Purdue University Indianapolis, Indianapolis, IN, USA
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Yunlong Liu
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Huanmei Wu
- Depart of BioHealth Informatics, School of Informatics and Computing, Indiana University-Purdue University Indianapolis, Indianapolis, IN, USA.
- Temple University College of Public Health, Philadelphia, PA, USA.
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9
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Weber S, Koschade SE, Hoffmann CM, Dubash TD, Giessler KM, Dieter SM, Herbst F, Glimm H, Ball CR. The notch target gene HEYL modulates metastasis forming capacity of colorectal cancer patient-derived spheroid cells in vivo. BMC Cancer 2019; 19:1181. [PMID: 31796022 PMCID: PMC6892194 DOI: 10.1186/s12885-019-6396-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 11/22/2019] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND While colorectal cancer (CRC) patients with localized disease have a favorable prognosis, the five-year-survival rate in patients with distant spread is still below 15%. Hence, a detailed understanding of the mechanisms regulating metastasis formation is essential to develop therapeutic strategies targeting metastasized CRC. The notch pathway has been shown to be involved in the metastatic spread of various tumor entities; however, the impact of its target gene HEYL remains unclear so far. METHODS In this study, we functionally assessed the association between high HEYL expression and metastasis formation in human CRC. Therefore, we lentivirally overexpressed HEYL in two human patient-derived CRC cultures differing in their spontaneous metastasizing capacity and analyzed metastasis formation as well as tumor cell dissemination into the bone marrow after xenotransplantation into NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ (NSG) mice. RESULTS HEYL overexpression decreased tumor cell dissemination and the absolute numbers of formed metastases in a sub-renal capsular spontaneous metastasis formation model, addressing all steps of the metastatic cascade. In contrast, metastatic capacity was not decreased following intrasplenic xenotransplantation where the cells are placed directly into the blood circulation. CONCLUSION These results suggest that HEYL negatively regulates metastasis formation in vivo presumably by inhibiting intravasation of metastasis-initiating cells.
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Affiliation(s)
- Sarah Weber
- Translational Functional Cancer Genomics, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK) Frankfurt am Main, Frankfurt am Main, Germany.,Department of Hematology and Oncology, University Hospital Frankfurt, Frankfurt am Main, Germany
| | - Sebastian E Koschade
- German Cancer Consortium (DKTK) Frankfurt am Main, Frankfurt am Main, Germany.,Department of Hematology and Oncology, University Hospital Frankfurt, Frankfurt am Main, Germany
| | - Christopher M Hoffmann
- Translational Functional Cancer Genomics, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Taronish D Dubash
- Translational Functional Cancer Genomics, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Klara M Giessler
- Translational Functional Cancer Genomics, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sebastian M Dieter
- Translational Functional Cancer Genomics, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Dresden and German Cancer Research Center (DKFZ), Dresden, Germany
| | - Friederike Herbst
- Translational Functional Cancer Genomics, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Dresden and German Cancer Research Center (DKFZ), Dresden, Germany
| | - Hanno Glimm
- Translational Functional Cancer Genomics, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Dresden and German Cancer Research Center (DKFZ), Dresden, Germany.,Center for Personalized Oncology, University Hospital Carl Gustav Carus Dresden at TU Dresden, Dresden, Germany.,German Cancer Consortium (DKTK) Dresden, Dresden, Germany
| | - Claudia R Ball
- Translational Functional Cancer Genomics, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Heidelberg, Germany. .,Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Dresden and German Cancer Research Center (DKFZ), Dresden, Germany. .,Center for Personalized Oncology, University Hospital Carl Gustav Carus Dresden at TU Dresden, Dresden, Germany.
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Bacalini MG, Franceschi C, Gentilini D, Ravaioli F, Zhou X, Remondini D, Pirazzini C, Giuliani C, Marasco E, Gensous N, Di Blasio AM, Ellis E, Gramignoli R, Castellani G, Capri M, Strom S, Nardini C, Cescon M, Grazi GL, Garagnani P. Molecular Aging of Human Liver: An Epigenetic/Transcriptomic Signature. J Gerontol A Biol Sci Med Sci 2019; 74:1-8. [PMID: 29554203 DOI: 10.1093/gerona/gly048] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Indexed: 12/12/2022] Open
Abstract
The feasibility of liver transplantation from old healthy donors suggests that this organ is able to preserve its functionality during aging. To explore the biological basis of this phenomenon, we characterized the epigenetic profile of liver biopsies collected from 45 healthy liver donors ranging from 13 to 90 years old using the Infinium HumanMethylation450 BeadChip. The analysis indicates that a large remodeling in DNA methylation patterns occurs, with 8,823 age-associated differentially methylated CpG probes. Notably, these age-associated changes tended to level off after the age of 60, as confirmed by Horvath's clock. Using stringent selection criteria, we further identified a DNA methylation signature of aging liver including 75 genomic regions. We demonstrated that this signature is specific for liver compared to other tissues and that it is able to detect biological age-acceleration effects associated with obesity. Finally, we combined DNA methylation measurements with available expression data. Although the intersection between the two omic characterizations was low, both approaches suggested a previously unappreciated role of epithelial-mesenchymal transition and Wnt-signaling pathways in the aging of human liver.
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Affiliation(s)
| | - Claudio Franceschi
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Italy.,DIMES-Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum, Bologna, Italy.,CIG, Interdepartmental Center 'L. Galvani', Alma Mater Studiorum, Bologna, Italy
| | - Davide Gentilini
- Department of Brain and Behavioral Sciences, University of Pavia, Italy
| | - Francesco Ravaioli
- DIMES-Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum, Bologna, Italy
| | - Xiaoyuan Zhou
- Group of Clinical Genomic Networks, Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, PR China.,University of Chinese Academy of Sciences, Beijing, PR China.,Department of Neurology, University of San Francisco, California
| | - Daniel Remondini
- Department of Physics and Astronomy (DIFA) and INFN Sez. Bologna, Alma Mater Studiorum, Italy
| | | | - Cristina Giuliani
- Department of Biological Geological and Environmental Sciences, Laboratory of Molecular Anthropology and Centre for Genome Biology, University of Bologna, Italy
| | - Elena Marasco
- CIG, Interdepartmental Center 'L. Galvani', Alma Mater Studiorum, Bologna, Italy
| | - Noémie Gensous
- DIMES-Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum, Bologna, Italy
| | | | - Ewa Ellis
- Department of Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institutet, Stockholm, Sweden
| | - Roberto Gramignoli
- Department of Laboratory Medicine, Division of Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Gastone Castellani
- CIG, Interdepartmental Center 'L. Galvani', Alma Mater Studiorum, Bologna, Italy.,Department of Biological Geological and Environmental Sciences, Laboratory of Molecular Anthropology and Centre for Genome Biology, University of Bologna, Italy
| | - Miriam Capri
- DIMES-Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum, Bologna, Italy.,CIG, Interdepartmental Center 'L. Galvani', Alma Mater Studiorum, Bologna, Italy
| | - Stephen Strom
- Department of Laboratory Medicine, Karolinska Institute and Karolinska Universitetssjukhuset, Stockholm, Sweden
| | - Christine Nardini
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden.,CNR IAC "Mauro Picone", Roma, Italy.,Personal Genomics S.r.l., Verona, Italy
| | - Matteo Cescon
- General Surgery and Transplant Unit, Department of Medical and Surgical Sciences, Sant'Orsola-Malpighi Hospital, Bologna, Italy
| | | | - Paolo Garagnani
- DIMES-Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum, Bologna, Italy.,CIG, Interdepartmental Center 'L. Galvani', Alma Mater Studiorum, Bologna, Italy.,Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden.,Applied Biomedical Research Center, S. Orsola-Malpighi Polyclinic, Bologna, Italy.,Institute of Molecular Genetics (IGM)-CNR, Unit of Bologna, Italy.,Laboratory of Musculoskeletal Cell Biology, Rizzoli Orthopaedic Institute, Bologna, Italy
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11
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Sun N, Zhang J, Zhang C, Shi Y, Zhao B, Jiao A, Chen B. Using Illumina Infinium HumanMethylation 450K BeadChip to explore genome‑wide DNA methylation profiles in a human hepatocellular carcinoma cell line. Mol Med Rep 2018; 18:4446-4456. [PMID: 30221710 PMCID: PMC6172394 DOI: 10.3892/mmr.2018.9441] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 08/03/2018] [Indexed: 12/31/2022] Open
Abstract
Aberrant DNA methylation is the most common type of epigenetic alteration and is associated with many types of cancer. Although previous studies have provided a few novel DNA methylation markers in hepatocellular carcinoma (HCC), specific DNA methylation patterns and comparisons of the aberrant alterations in methylation between HCC and normal liver cell lines have not yet been reported. Therefore, in the present study the Illumina Infinium HumanMethylation 450K BeadChip was employed to identify the genome-wide aberrant DNA methylation profiles of Huh7 and L02 cells. Following Bonferroni adjustment, 102,254 differentially methylated CpG sites (covering 26,511 genes) were detected between Huh7 and L02 cells. Of those CpG sites, 62,702 (61.3%) sites were hypermethylated (covering 12,665 genes) and 39,552 (38.7%) sites were hypomethylated (covering 13,846 genes). The results of the present study indicated that 40.3% of the CpG sites were in CpG island regions, 20.7% were in CpG shores and 8.8% were in shelf regions. A total of 57.3% hypermethylated CpG sites and 39.4% of the hypomethylated CpG sites had a |β-Difference| ≥50%. Within the significant differentially methylated CpG sites, 490 genes were located within 598 differentially methylated regions. Gene Ontology enrichment analysis revealed that 2,107 differentially methylated genes were associated with ‘biological process’, 13,351 differentially methylated genes were associated with ‘molecular function’, and 18,041 differentially methylated genes were associated with ‘cellular component’. Kyoto Encyclopedia of Genes and Genomes pathway-based analysis revealed 43 signaling pathways that were associated with 5,195 differentially methylated genes. These results demonstrated that aberrant DNA methylation may be a key and common event underlying the tumorigenesis of Huh7 cells. The present study also identified many subsets of hypo- or hyper-methylated CpG sites, genes and signaling pathways, which have an importance in the occurrence and development of HCC.
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Affiliation(s)
- Ning Sun
- Department of Hepatobiliary and Transplantation Surgery, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning 110001, P.R. China
| | - Jialin Zhang
- Department of Hepatobiliary and Transplantation Surgery, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning 110001, P.R. China
| | - Chengshuo Zhang
- Department of Hepatobiliary and Transplantation Surgery, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning 110001, P.R. China
| | - Yue Shi
- Department of Hepatobiliary and Transplantation Surgery, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning 110001, P.R. China
| | - Bochao Zhao
- Department of Hepatobiliary and Transplantation Surgery, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning 110001, P.R. China
| | - Ao Jiao
- Department of Hepatobiliary and Transplantation Surgery, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning 110001, P.R. China
| | - Baomin Chen
- Department of Hepatobiliary and Transplantation Surgery, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning 110001, P.R. China
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12
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Boyle M, Mann J. WITHDRAWN: Epigenetics in Chronic Liver Disease. J Hepatol 2017:S0168-8278(17)32255-9. [PMID: 28855099 DOI: 10.1016/j.jhep.2017.08.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 08/17/2017] [Accepted: 08/18/2017] [Indexed: 12/04/2022]
Abstract
This article has been withdrawn at the request of the editors. The Publisher apologizes for any inconvenience this may cause. The full Elsevier Policy on Article Withdrawal can be found at https://www.elsevier.com/about/our-business/policies/article-withdrawal.
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Affiliation(s)
- Marie Boyle
- Institute of Cellular Medicine, Faculty of Medical Sciences, 4(th) Floor, William Leech Building, Newcastle University, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK
| | - Jelena Mann
- Institute of Cellular Medicine, Faculty of Medical Sciences, 4(th) Floor, William Leech Building, Newcastle University, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK.
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13
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Seok Y, Kang HG, Lee SY, Jeong JY, Choi JE, Jung DK, Jin CC, Hong MJ, Do SK, Lee WK, Park JY, Shin KM, Yoo SS, Lee J, Cho S, Cha SI, Kim CH, Jheon S, Lee EB, Park JY. Polymorphisms in Epithelial-Mesenchymal Transition-Related Genes and the Prognosis of Surgically Treated Non-small Cell Lung Cancer. Ann Surg Oncol 2017; 24:3386-3395. [PMID: 28766235 DOI: 10.1245/s10434-017-6002-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Indexed: 12/19/2022]
Abstract
BACKGROUND This study was conducted to determine whether single-nucleotide polymorphisms (SNPs) in EMT-related genes may influence the prognosis of NSCLC after surgery. METHODS There were 88 SNPs in EMT-related genes evaluated in a discovery set of 376 patients who underwent curative surgery for NSCLC. Significantly, 14 SNPs were evaluated in a validation set of 428 patients. Luciferase assay and RT-PCR were conducted to examine functional relevance of polymorphisms. RESULTS Fourteen SNPs that were associated with survival outcomes in a discovery set were selected for validation. Among those, two SNPs (FOXF2 rs1711972A>C and HEYL rs784621G>A) were replicated in a validation study. In combined analysis, FOXF2 rs1711972 AC+CC genotype was associated with significantly better overall survival (OS) and disease-free survival (DFS) compared with AA genotype (adjusted hazard ratio [aHR] for OS = 0.67, 95% confidence interval [CI] 0.51-0.88, P = 0.004; and aHR for DFS = 0.77, 95% CI 0.62-0.95, P = 0.01). HEYL rs784621 AA genotype exhibited a significantly worse OS compared with GG+GA genotype (aHR for OS = 2.65, 95% CI 1.63-4.31, P = 8 × 10-5). FOXF2 rs1711972C allele had a significantly increased promoter activity than rs1711972A allele (P = 0.01), and HEYL rs784621A allele had a significantly lower promoter activity than rs784621G allele (P = 0.004). FOXF2 rs1711972A>C was significantly associated with increased FOXF2 mRNA expression. CONCLUSIONS FOXF2 rs1711972A>C and HEYL rs784621G>A were associated with survival outcomes of surgically treated NSCLC. These SNPs may help to identify patients at high risk of poor disease outcomes.
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Affiliation(s)
- Yangki Seok
- Lung Cancer Center, Kyungpook National University Medical Center, Daegu, Republic of Korea.,Department of Thoracic Surgery, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Hyo-Gyoung Kang
- Department of Biochemistry and Cell Biology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea.,Cell and Matrix Research Institute, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Shin Yup Lee
- Lung Cancer Center, Kyungpook National University Medical Center, Daegu, Republic of Korea.,Department of Internal Medicine, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Ji Yun Jeong
- Department of Pathology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Jin Eun Choi
- Department of Biochemistry and Cell Biology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea.,Cell and Matrix Research Institute, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Deuk Kju Jung
- Department of Biochemistry and Cell Biology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea.,BK21 Plus KNU Biomedical Convergence Program, Department of Biomedical Science, Kyungpook National University, Daegu, Republic of Korea
| | - Cheng Cheng Jin
- Department of Biochemistry and Cell Biology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea.,BK21 Plus KNU Biomedical Convergence Program, Department of Biomedical Science, Kyungpook National University, Daegu, Republic of Korea
| | - Mi Jeong Hong
- Department of Biochemistry and Cell Biology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea.,BK21 Plus KNU Biomedical Convergence Program, Department of Biomedical Science, Kyungpook National University, Daegu, Republic of Korea
| | - Sook Kyung Do
- Department of Biochemistry and Cell Biology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea.,BK21 Plus KNU Biomedical Convergence Program, Department of Biomedical Science, Kyungpook National University, Daegu, Republic of Korea
| | - Won Kee Lee
- Biostatistics Medical Research Collaboration Center, Kyungpook National University Hospital and Kyungpook National University School of Medicine, Daegu, Republic of Korea
| | - Ji Young Park
- Department of Pathology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Kyung Min Shin
- Department of Radiology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Seung Soo Yoo
- Lung Cancer Center, Kyungpook National University Medical Center, Daegu, Republic of Korea.,Department of Internal Medicine, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Jaehee Lee
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Sukki Cho
- Department of Thoracic and Cardiovascular Surgery, Seoul National University School of Medicine, Seoul, Republic of Korea
| | - Seung Ick Cha
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Chang Ho Kim
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Sanghoon Jheon
- Department of Thoracic and Cardiovascular Surgery, Seoul National University School of Medicine, Seoul, Republic of Korea
| | - Eung Bae Lee
- Lung Cancer Center, Kyungpook National University Medical Center, Daegu, Republic of Korea. .,Department of Thoracic Surgery, School of Medicine, Kyungpook National University, Daegu, Republic of Korea.
| | - Jae Yong Park
- Lung Cancer Center, Kyungpook National University Medical Center, Daegu, Republic of Korea. .,Department of Biochemistry and Cell Biology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea. .,Cell and Matrix Research Institute, School of Medicine, Kyungpook National University, Daegu, Republic of Korea. .,Department of Internal Medicine, School of Medicine, Kyungpook National University, Daegu, Republic of Korea. .,BK21 Plus KNU Biomedical Convergence Program, Department of Biomedical Science, Kyungpook National University, Daegu, Republic of Korea.
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14
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Liu Z, Sanders AJ, Liang G, Song E, Jiang WG, Gong C. Hey Factors at the Crossroad of Tumorigenesis and Clinical Therapeutic Modulation of Hey for Anticancer Treatment. Mol Cancer Ther 2017; 16:775-786. [PMID: 28468863 DOI: 10.1158/1535-7163.mct-16-0576] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2016] [Revised: 12/29/2016] [Accepted: 12/29/2016] [Indexed: 11/16/2022]
Affiliation(s)
- Zihao Liu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetic and Gene Regulation, Breast Tumor Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Andrew J Sanders
- Cardiff China Medical Research Collaborative, Cardiff University School of Medicine, Cardiff University, Heath Park, Cardiff, United Kingdom
| | - Gehao Liang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetic and Gene Regulation, Breast Tumor Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Erwei Song
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetic and Gene Regulation, Breast Tumor Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Wen G Jiang
- Cardiff China Medical Research Collaborative, Cardiff University School of Medicine, Cardiff University, Heath Park, Cardiff, United Kingdom.
| | - Chang Gong
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetic and Gene Regulation, Breast Tumor Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China.
- Cardiff China Medical Research Collaborative, Cardiff University School of Medicine, Cardiff University, Heath Park, Cardiff, United Kingdom
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15
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Cantelli G, Crosas-Molist E, Georgouli M, Sanz-Moreno V. TGFΒ-induced transcription in cancer. Semin Cancer Biol 2017; 42:60-69. [PMID: 27586372 PMCID: PMC6137079 DOI: 10.1016/j.semcancer.2016.08.009] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 08/19/2016] [Indexed: 12/15/2022]
Abstract
The Transforming Growth Factor-beta (TGFβ) pathway mediates a broad spectrum of cellular processes and is involved in several diseases, including cancer. TGFβ has a dual role in tumours, acting as a tumour suppressor in the early phase of tumorigenesis and as a tumour promoter in more advanced stages. In this review, we discuss the effects of TGFβ-driven transcription on all stages of tumour progression, with special focus on lung cancer. Since some TGFβ target genes are specifically involved in promoting metastasis, we speculate that these genes might be good targets to block tumour progression without compromising the tumour suppressor effects of the TGFβ pathway.
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Affiliation(s)
- Gaia Cantelli
- Tumour Plasticity Laboratory, Randall Division of Cell and Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London SE1 1UL, UK
| | - Eva Crosas-Molist
- Tumour Plasticity Laboratory, Randall Division of Cell and Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London SE1 1UL, UK
| | - Mirella Georgouli
- Tumour Plasticity Laboratory, Randall Division of Cell and Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London SE1 1UL, UK
| | - Victoria Sanz-Moreno
- Tumour Plasticity Laboratory, Randall Division of Cell and Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London SE1 1UL, UK.
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16
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Yokobori T, Nishiyama M. TGF-β Signaling in Gastrointestinal Cancers: Progress in Basic and Clinical Research. J Clin Med 2017; 6:jcm6010011. [PMID: 28106769 PMCID: PMC5294964 DOI: 10.3390/jcm6010011] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 12/31/2016] [Accepted: 01/16/2017] [Indexed: 12/18/2022] Open
Abstract
Transforming growth factor (TGF)-β superfamily proteins have many important biological functions, including regulation of tissue differentiation, cell proliferation, and migration in both normal and cancer cells. Many studies have reported that TGF-β signaling is associated with disease progression and therapeutic resistance in several cancers. Similarly, TGF-β-induced protein (TGFBI)—a downstream component of the TGF-β signaling pathway—has been shown to promote and/or inhibit cancer. Here, we review the state of basic and clinical research on the roles of TGF-β and TGFBI in gastrointestinal cancers.
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Affiliation(s)
- Takehiko Yokobori
- Research Program for Omics-based Medical Science, Division of Integrated Oncology Research, Gunma University Initiative for Advanced Research, 3-39-22 Showa-machi, Maebashi, Gunma 371-8511, Japan.
| | - Masahiko Nishiyama
- Research Program for Omics-based Medical Science, Division of Integrated Oncology Research, Gunma University Initiative for Advanced Research, 3-39-22 Showa-machi, Maebashi, Gunma 371-8511, Japan.
- Department of Molecular Pharmacology and Oncology, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi, Gunma 371-8511, Japan.
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17
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Lee SM, Kim-Ha J, Choi WY, Lee J, Kim D, Lee J, Choi E, Kim YJ. Interplay of genetic and epigenetic alterations in hepatocellular carcinoma. Epigenomics 2016; 8:993-1005. [PMID: 27411963 DOI: 10.2217/epi-2016-0027] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Genetic and epigenetic alterations play prominent roles in hepatocarcinogenesis and their appearance varies depending on etiological factors, race and tumor progression. Intriguingly, distinct patterns of these genetic and epigenetic mutations are coupled not only to affect each other, but to trigger different types of tumorigenesis. The patterns and frequencies of somatic variations vary depending on the nature of the surrounding chromatin. On the other hand, epigenetic alterations often induce genomic instability prone to mutation. Therefore, genetic mutations and epigenetic alterations in hepatocellular carcinoma appear to be inseparable factors that accelerate tumorigenesis synergistically. We have summarized recent findings on genetic and epigenetic modifications, their influences on each other's alterations and putative roles in liver tumorigenesis.
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Affiliation(s)
- Sun-Min Lee
- Department of Biochemistry, College of Life Science & Technology, Yonsei University, Seoul, Korea
| | - Jeongsil Kim-Ha
- Department of Integrative Bioscience & Biotechnology, College of Life Sciences, Sejong University, Seoul, Korea
| | - Won-Young Choi
- Department of Integrated Omics for Biomedical Science, Graduate School, Yonsei University, Seoul, Korea
| | - Jungwoo Lee
- Department of Integrated Omics for Biomedical Science, Graduate School, Yonsei University, Seoul, Korea
| | - Dawon Kim
- Department of Integrated Omics for Biomedical Science, Graduate School, Yonsei University, Seoul, Korea
| | - Jinyoung Lee
- Department of Integrated Omics for Biomedical Science, Graduate School, Yonsei University, Seoul, Korea
| | - Eunji Choi
- Department of Integrated Omics for Biomedical Science, Graduate School, Yonsei University, Seoul, Korea
| | - Young-Joon Kim
- Department of Biochemistry, College of Life Science & Technology, Yonsei University, Seoul, Korea.,Department of Integrated Omics for Biomedical Science, Graduate School, Yonsei University, Seoul, Korea
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